Oligonucleotides targeting rna binding protein sites

Abstract

The present invention relates to antisense oligonucleotides which are complementary to conserved TDP-43 binding sites on pre-mRNA transcripts, which are capable of restoring RNA binding protein function in the processing of multiple independent mRNAs in TDP-43 depleted cells.

1 . A method of treating a disease characterized by TDP-43 pathology in a subject in need thereof, the method comprising administering to the subject an antisense oligonucleotide, of 8 to 40 nucleotides in length, which comprises a contiguous nucleotide sequence of at least 8 nucleotides in length with at least 90% complementarity to a sequence selected from the group consisting of (5′-3′) (UG)n, (GU)n, wherein n is 4-20, UGUGUGUG, UGUGUGUGU, UGUGUGUGUG, UGUGUGUGUGU, UGUGUGUGUGUG, UGUGUGUGUGUGU, GUGUGUGU, GUGUGUGUG, GUGUGUGUGU, GUGUGUGUGUGU, GUGUGUGUGUGUG, and GUGAAUGA, wherein the TDP-43 pathology is a neurological disorder. 
     
     
         2 . The method according to  claim 1 , wherein the contiguous nucleotide sequence comprises one or more modified nucleosides. 
     
     
         3 . The method according to  claim 1 , wherein the contiguous nucleotide sequence comprises SEQ ID NO: 27. 
     
     
         4 . The method according to  claim 1 , wherein the contiguous nucleotide sequence is at least 12 nucleotides in length. 
     
     
         5 . The method according to  claim 1 , wherein the antisense oligonucleotide does not comprise a region of more than 3, or more than 4, contiguous DNA nucleosides. 
     
     
         6 . The method according to  claim 2 , wherein the one or more modified nucleosides, is a 2′ sugar modified nucleoside, such as a 2′ sugar modified nucleoside independently selected from the group consisting of 2′-O-alkyl-RNA; 2′-O-methyl RNA (2′-OMe); 2′-alkoxy-RNA; 2′-O-methoxyethyl-RNA (2′-MOE); 2′-amino-DNA; 2′-fluro-RNA; 2′-fluoro-DNA; arabino nucleic acid (ANA); 2′-fluoro-ANA; locked nucleic acid (LNA), and any combination thereof. 
     
     
         7 . The method according to  claim 6 , wherein the 2′ sugar modified nucleoside is an affinity enhancing 2′ sugar modified nucleoside. 
     
     
         8 . The method according to  claim 2 , wherein the contiguous nucleotide sequence of the antisense oligonucleotide comprises 2′-O-methoxyethyl-RNA (2′-MOE) nucleosides. 
     
     
         9 . The method according to  claim 8 , wherein all the nucleosides of the contiguous nucleotide sequence are 2′-O-methoxyethyl-RNA (2′-MOE) nucleosides. 
     
     
         10 . The method according to  claim 9 , wherein all the contiguous nucleotide sequence of the antisense oligonucleotide are linked by phosphorothioate internucleoside linkages. 
     
     
         11 . The method according to  claim 2 , wherein one or more of the modified nucleosides is a locked nucleic acid nucleoside (LNA). 
     
     
         12 . The method according to  claim 11 , wherein the LNA nucleoside is selected from the group consisting of constrained ethyl nucleoside (cEt), and β-Doxy-LNA. 
     
     
         13 . The method according to  claim 2 , wherein the contiguous nucleotide sequence of the antisense oligonucleotide comprises or consists of LNA nucleosides and DNA nucleosides. 
     
     
         14 . The method according to  claim 2 , wherein the antisense oligonucleotide or contiguous nucleotide sequence thereof is a mixmer or a totalmer. 
     
     
         15 . The method according to  claim 2 , wherein the cytosine bases present in the antisense oligonucleotide or contiguous nucleotide sequence thereof are independently selected from the group consisting of cytosine and 5-methyl cytosine. 
     
     
         16 . The method according to  claim 2 , wherein one or more of the internucleoside linkages positioned between the nucleosides on the contiguous nucleotide sequence are modified. 
     
     
         17 . The method according to  claim 16 , wherein one or more, or all of the modified internucleoside linkages comprise a phosphorothioate linkage. 
     
     
         18 . The method according to  claim 2 , wherein all the internucleoside linkages present in the antisense oligonucleotide are phosphorothioate internucleoside linkages. 
     
     
         19 . The method according to  claim 1 , wherein the length of the contiguous nucleotide sequence is 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. 
     
     
         20 . The method according to  claim 1 , wherein the antisense oligonucleotide consists of the contiguous nucleotide sequence. 
     
     
         21 . The method according to  claim 1 , wherein the antisense oligonucleotide is formulated as a pharmaceutically acceptable salt. 
     
     
         22 . The method according to  claim 21 , wherein the pharmaceutically acceptable salt is a sodium salt or a potassium salt. 
     
     
         23 . The method according to  claim 1 , wherein the antisense oligonucleotide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition comprises the antisense oligonucleotide and a pharmaceutically acceptable diluent, solvent, carrier, salt, and/or adjuvant. 
     
     
         24 . The method according to  claim 1 , wherein the neurological disorder is amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), Progressive supranuclear palsy (PSP), Primary lateral sclerosis, Progressive muscular atrophy, Alzheimer's disease, Parkinsons disease, Autism, Hippocampal sclerosis dementia, Down syndrome, Huntington's disease, a polyglutamine disease, spinocerebellar ataxia 3, a myopathy, or Chronic Traumatic Encephalopathy. 
     
     
         25 . A method of treating a disease characterized by TDP-43 pathology in a subject in need thereof, the method comprising administering to the subject a conjugate comprising:
 (i) an antisense oligonucleotide, of 8 to 40 nucleotides in length, which comprises a contiguous nucleotide sequence of at least 8 nucleotides in length with at least 90% complementarity to a sequence selected from the group consisting of (5′-3′) (UG)n, (GU)n, wherein n is 4-20, UGUGUGUG, UGUGUGUGU, UGUGUGUGUG, UGUGUGUGUGU, UGUGUGUGUGUG, UGUGUGUGUGUGU, GUGUGUGU, GUGUGUGUG, GUGUGUGUGU, GUGUGUGUGUGU, GUGUGUGUGUGUG, and GUGAAUGA; and   (ii) at least one conjugate moiety covalently attached to said oligonucleotide, and wherein the TDP-43 pathology is a neurological disorder.   
     
     
         26 . The method according to  claim 25 , wherein the antisense oligonucleotide is formulated as a pharmaceutically acceptable salt. 
     
     
         27 . The method according to  claim 26 , wherein the pharmaceutically acceptable salt is a sodium salt or a potassium salt. 
     
     
         28 . The method according to  claim 25 , wherein the antisense oligonucleotide is formulated as a pharmaceutical composition, wherein the pharmaceutical composition comprises the antisense oligonucleotide and a pharmaceutically acceptable diluent, solvent, carrier, salt, and/or adjuvant. 
     
     
         29 . The method according to  claim 25 , wherein the neurological disorder is amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), Progressive supranuclear palsy (PSP), Primary lateral sclerosis, Progressive muscular atrophy, Alzheimer's disease, Parkinsons disease, Autism, Hippocampal sclerosis dementia, Down syndrome, Huntington's disease, a polyglutamine disease, spinocerebellar ataxia 3, a myopathy, or Chronic Traumatic Encephalopathy.